Gareth Roberts

Identification of a new class of cytochrome P450 from a Rhodococcus sp.

A degenerate set of PCR primers were used to clone a gene encoding a cytochrome P450 (the P450RhF gene) from Rhodococcus sp. strain NCIMB 9784 which is of unique primary structural organization. Surprisingly, analysis of the translation product revealed that the P450 is fused to a reductase domain at the C terminus which displays sequence conservation for dioxygenase reductase proteins. The reductase partner comprises flavin mononucleotide- and NADH-binding motifs and a [2Fe2S] ferredoxin-like center. The gene was engineered for heterologous expression in Escherichia coli, and conditions were found in which the enzyme was produced in a soluble form. A recombinant strain of E. coli was able to mediate the O dealkylation of 7-ethoxycoumarin in good yield, despite the absence of any recombinant redox proteins. This unprecedented finding leads us to propose that P450RhF represents the first example of a new class of cytochromes P450 in which the reducing equivalents are supplied by a novel reductase in a fused arrangement.

Analysis of the domain properties of the novel cytochrome P450 RhF.

The properties of the heme, flavin mononucleotide (FMN) and FeS domains of P450 RhF, from Rhodococcus sp. NCIMB 9784, expressed separately and in combination are analysed. The nucleotide preference, imidazole binding and reduction potentials of the heme and FMN domains are unaltered by their separation. The intact enzyme is monomeric and the flavin is confirmed to be FMN. The two one‐electron reduction potentials of the FMN are −240 and −270 mV. The spectroscopic and thermodynamic properties of the FeS domain, masked in the intact enzyme, are revealed for the first time, confirming it as a 2Fe–2S ferredoxin with a reduction potential of −214 mV.

How communication changes when we cannot mime the world: Experimental evidence for the effect of iconicity on combinatoriality.

Communication systems are exposed to two different pressures: a pressure for transmission efficiency, such that messages are simple to produce and perceive, and a pressure for referential efficiency, such that messages are easy to understand with their intended meaning. A solution to the first pressure is combinatoriality--the recombination of a few basic meaningless forms to express an infinite number of meanings. A solution to the second is iconicity--the use of forms that resemble what they refer to. These two solutions appear to be incompatible with each other, as iconic forms are ill-suited for use as meaningless combinatorial units. Furthermore, in the early stages of a communication system, when basic referential forms are in the process of being established, the pressure for referential efficiency is likely to be particularly strong, which may lead it to trump the pressure for transmission efficiency. This means that, where iconicity is available as a strategy, it is likely to impede the emergence of combinatoriality. Although this hypothesis seems consistent with some observations of natural language, it was unclear until recently how it could be soundly tested. This has changed thanks to the development of a line of research, known as Experimental Semiotics, in which participants construct novel communication systems in the laboratory using an unfamiliar medium. We conducted an Experimental Semiotic study in which we manipulated the opportunity for iconicity by varying the kind of referents to be communicated, while keeping the communication medium constant. We then measured the combinatoriality and transmission efficiency of the communication systems. We found that, where iconicity was available, it provided scaffolding for the construction of communication systems and was overwhelmingly adopted. Where it was not available, however, the resulting communication systems were more combinatorial and their forms more efficient to produce. This study enriches our understanding of the fundamental design principles of human communication and contributes tools to enrich it further.

Probing the substrate specificity of the catalytically self-sufficient cytochrome P450 RhF from a Rhodococcus sp.

Analysis of the substrate specificity of the self-sufficient cytochrome P450 RhF revealed that the enzyme tends to catalyse the dealkylation of substituted alkyl-aryl ethers with shorter alkyl moieties more readily than equivalent compounds with longer alkyl groups.

The emergence of duality of patterning: Insights from the laboratory

Abstract The concept of duality of patterning (henceforth DP) has recently begun to undergo new scrutiny. In particular, the fact that Al-Sayyid Bedouin Sign Language (ABSL) does not appear to exhibit a layer of meaningless units (Sandler et al. 2011) casts doubt on the universality of DP as a defining feature of natural language. Why, then, do the vast majority of the worlds languages exhibit DP? Two hypotheses have been suggested. The first is that DP is a necessary solution to the problem of conveying a large number of meanings; the second is that DP arises as a consequence of conventionalization. We tested these hypotheses in an experimental-semiotics study. Our results supported the hypothesis based on conventionalization but were inconclusive with regard to the hypothesis based on the number of meanings. At the same time, the task of measuring DP in an experimental-semiotics study presented interesting challenges, suggesting that the concept of DP may need some overhauling.

Do We Notice when Communication Goes Awry? An Investigation of People's Sensitivity to Coherence in Spontaneous Conversation

In the dominant theoretical framework, human communication is modeled as the faithful transmission of information. This implies that when people are involved in communicational exchanges, they should be sensitive to the success with which information is transmitted, easily detecting when conversations lack coherence. The expectation that humans are good at detecting conversational incoherence is in line with common intuition, but there are several reasons to suspect that it might be unrealistic. First, similar intuitions have been shown to be unrealistic for a number of psychological processes. Second, faithful information transmission may conflict with other conversational goals. Third, mechanisms supporting information transmission may themselves lead to cases of incoherence being missed. To ascertain the extent to which people are insensitive to patches of serious conversational incoherence, we generated such patches in the laboratory by repeatedly crossing two unrelated conversations. Across two studies, involving both narrowly and broadly focused conversations, between 27% and 42% of the conversants did not notice that their conversations had been crossed. The results of these studies suggest that it may indeed be unrealistic to model spontaneous conversation as faithful information transmission. Rather, our results are more consistent with models of communication that view it as involving noisy and error-prone inferential processes, serving multiple independent goals.

The Type I Restriction Enzymes as Barriers to Horizontal Gene Transfer: Determination of the DNA Target Sequences Recognised by Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complexes 133/ST771 and 398

The Type I DNA restriction-modification (RM) systems of Staphylococcus aureus are known to act as a significant barrier to horizontal gene transfer between S. aureus strains belonging to different clonal complexes. The livestock-associated clonal complexes CC133/771 and CC398 contain Type I RM systems not found in human MRSA strains as yet but at some point transfer will occur. When this does take place, horizontal gene transfer of resistance will happen more easily between these strains. The reservoir of antibiotic resistance, virulence and host-adaptation genes present in livestock-associated MRSA will then potentially contribute to the development of newly evolving MRSA clones. The target sites recognised by the Type I RM systems of CC133/771 and CC398 were identified as CAG(N)5RTGA and ACC(N)5RTGA, respectively. Assuming that these enzymes recognise the methylation state of adenine, the underlined A and T bases indicate the unique positions of methylation. Target methylation points for enzymes from CC1 were also identified. The methylation points for CC1-1 are CCAY(N)5TTAA and those for CC1-2 are CCAY(N)6 TGT with the underline indicating the adenine methylation site thus clearing up the ambiguity noted previously (Roberts et al. 2013, Nucleic Acids Res 41:7472-7484) for the half sites containing two adenine bases.

Perspectives on Language as a Source of Social Markers

Because linguistic forms vary between groups of speakers, language serves as a source of social markers, allowing people to distinguish between those who do and do not belong to the same social group. This review surveys interdisciplinary perspectives on four issues concerning social markers: (a) the role of inter- and intra-individual variation, (b) the purpose of social markers, (c) language as an especially good source of social markers and (d) social marking as a source of new dialects.

DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.

Abstract Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction–modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range of biochemical assays on purified enzymes and single molecule real-time sequencing on genomic DNA to determine these target sequences and their patterns of methylation. Knowledge of the main target sequences for Sau1 will facilitate the synthesis of new vectors for transformation of the most prevalent lineages of this ‘untransformable’ bacterium.

The linguist’s Drosophila: Experiments in language change

Abstract Although experimental methods are used in the study of language change, it has been claimed that there is no analogue of the biologist’s Drosophila – no means, in other words, of observing change in the laboratory. Here it is argued that this pessimism is unwarranted, and that there is in fact something equivalent: a set of experimental methods developed originally to study the emergence and evolution of language, and which involve the use of novel “laboratory languages” to play games with a social component. These methods are described, and arguments are made in favor of their broader application to questions of change in modern language. Ideally (as has begun to occur in a few cases) this should involve interdisciplinary collaborations, and it would both open new doors for the testing of hypotheses and bring researchers in the field of language evolution into contact with a vast store of real-world data. Concerns about the authenticity of laboratory data are not unreasonable, but less pressing than might be imagined, and in fact should call for precisely the kind of interdisciplinary approach advocated here. This can only benefit everyone involved.